Pharmacology and Neuroscience
DISCLAIMER: Since companies and universities change URL addresses often, the accuracy or completeness of any link listed is not guaranteed.
Sources for pre-spotted arrays which are compatible with the GenePix 4000 scanner
- CLONTECH(human, mouse, rat)
- Mergen Ltd. (human, mouse, rat, S. Aureus)
- PerkinElmer-NEN Life Sciences (human, mouse)
- Ontario Cancer Institute(human, mouse, yeast)
- OriGene Technologies (human with homology to mouse)
- Phase-1 Molecular Toxicology (human, dog, rat; click on Products)
- Takara (human, rat, mouse, plant, bacteria; available through Fisher, search their web site using "microarrays")
- MWG Biotech (human, rat, mouse, zebrafish, yeast, E. coli, H. pylori; select region, click on catalog arrays in Products list)
- Center for Applied Genomics(human, rat, Mycobacterium tuberculosis)
- Agilent Technologies(human, mouse, rat, Arabidopsis thaliana; see Products & Services)
- Scienion (human, specialized chips, click on Products)
- Amersham biosciences (CodeLink Bioarray systems, human, rat, mouse)
- Advanced Array Technology (rat, Staphlococcus; Specialized chips)
- ArrayIt(human, mouse, rat)
- Keck Microarray Resource at Yale (human, mouse, rat, Arabidopsis)
- SuperArray Bioscience Corp. (human and mouse)
See also NIH site for non-commercial and commercial sites: NIH microarray platform list
Sources for microarray data analysis freeware and public domain database mining programs
(several sites that offer software free to academics require registration)
Data storage and analysis, ontology searches, probe searches
- CLUSTER, TreeView, and J-Express (site for J-express installation)
- XCluster
- Plaid Models
- BRB ArrayTools
- SVDMAN (Singular Value Decomposition for Microarray Analysis)
- KNNimpute (for the estimation of missing values in gene microarray data)
- Timewarp programs (for aligning gene expression time series with time warping algorithms)
- Cyber-T, GeneX, others (various programs developed at UC Irvine, including Cyber-T for statistics)
- SMD (Stanford Microarray Database resource)
- SAM (for statistical analysis of microarrays)
- PAM (predictive analysis for microarrays)
- EMMIX-GENE (see Bioinformatics, 18: 413-422, 2002) GeneANOVA (see Bioinformatics, 18: 490-491, 2002)
- DAVID and EASE (for annotation and analysis of genome-scale datasets)
- AMAD database storage program
- AMADA
- GenMAPP (Molecular Array Pathway Profiles)
- MAPS (MicroArray Project System)
- GeneInfoMatic (database searching by accession numbers)
- Pubgene (ontology)
- GeneX (gene expression database and analysis server)
- ProbeMatch database (accessible by clicking the ‘Query ProbeMatchDB’ link)
- Onto-Express (searches databases for annotation and functions of human and mouse genes inputted as differenetially regulated)
- BASE (Bio Array Software Environment)
- mouse GO (gene ontology database from the Mouse Genome Informatics group)
- GEDA Gene Expression Data Analysis Tool
- TM4 Package (TIGR's software)
- GSCope (a software package offered by the RIKEN in Japan)
- Longhorn Array Database (similar to SMD but runs on Linux-based PCs)
Other
- Jellyfish (similar to VectorNT)
- Quantitative 'real time' PCR site (with primers for 'housekeeping' genes)
Source for gaining membership on the Gene-Arrays list server and Real time PCR (Taqman) list server and searching their archives.
Gateways to a lot of other information about DNA array users, producers, and resources. (KEGG is for genes and genomes)
Return to home page Last updated on June 15, 2004